forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9788 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
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commit
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@ -195,7 +195,7 @@ are point particles. See the discussion of ellipsoidflag and the
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</P>
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<UL><LI><I>Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies</I> = atom-property sections
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<LI><I>Bonds, Angles, Dihedrals, Impropers</I> = molecular topology sections
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<LI><I>Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
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<LI><I>Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs</I> = force field sections
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<LI><I>BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs</I> = class 2 force field sections
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</UL>
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<P>Each section is listed below in alphabetic order. The format of each
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@ -814,8 +814,42 @@ e.g. <A HREF = "atom_style.html">atom_style sphere</A>.
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</UL>
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<P>The number and meaning of the coefficients are specific to the defined
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pair style. See the <A HREF = "pair_style.html">pair_style</A> and
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<A HREF = "pair_coeff.html">pair_coeff</A> commands for details. Coefficients can
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also be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
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<A HREF = "pair_coeff.html">pair_coeff</A> commands for details. Since pair
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coefficients for types I != J are not specified, these will be
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generated automatically by the pair style's mixing rule. See the
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individual pair_style doc pages and the <A HREF = "pair_modify.html">pair_modify
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mix</A> command for details. Pair coefficients can also
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be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
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script.
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</P>
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<HR>
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<P><I>PairIJ Coeffs</I> section:
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</P>
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<UL><LI>one line per pair of atom types for all I,J with I <= J
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<LI>line syntax: ID1 ID2 coeffs
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<PRE> ID1 = atom type I = 1-N
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ID2 = atom type J = I-N, with I <= J
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coeffs = list of coeffs
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</PRE>
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<LI>examples:
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<PRE> 3 3 0.022 2.35197 0.022 2.35197
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3 5 0.022 2.35197 0.022 2.35197
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</PRE>
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</UL>
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<P>This section must have N*(N+1)/2 lines where N = # of atom types. The
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number and meaning of the coefficients are specific to the defined
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pair style. See the <A HREF = "pair_style.html">pair_style</A> and
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<A HREF = "pair_coeff.html">pair_coeff</A> commands for details. Since pair
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coefficients for types I != J are all specified, these values will
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turn off the default mixing rule defined by the pair style. See the
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individual pair_style doc pages and the <A HREF = "pair_modify.html">pair_modify
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mix</A> command for details. Pair coefficients can also
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be set via the <A HREF = "pair_coeff.html">pair_coeff</A> command in the input
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script.
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</P>
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<HR>
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@ -189,7 +189,7 @@ These are the section keywords for the body of the file.
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{Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies} = atom-property sections
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{Bonds, Angles, Dihedrals, Impropers} = molecular topology sections
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{Pair Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
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{Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, \
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Improper Coeffs} = force field sections
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{BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, \
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EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, \
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@ -716,8 +716,37 @@ example: :l
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The number and meaning of the coefficients are specific to the defined
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pair style. See the "pair_style"_pair_style.html and
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"pair_coeff"_pair_coeff.html commands for details. Coefficients can
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also be set via the "pair_coeff"_pair_coeff.html command in the input
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"pair_coeff"_pair_coeff.html commands for details. Since pair
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coefficients for types I != J are not specified, these will be
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generated automatically by the pair style's mixing rule. See the
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individual pair_style doc pages and the "pair_modify
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mix"_pair_modify.html command for details. Pair coefficients can also
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be set via the "pair_coeff"_pair_coeff.html command in the input
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script.
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:line
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{PairIJ Coeffs} section:
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one line per pair of atom types for all I,J with I <= J :ulb,l
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line syntax: ID1 ID2 coeffs :l
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ID1 = atom type I = 1-N
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ID2 = atom type J = I-N, with I <= J
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coeffs = list of coeffs :pre
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examples: :l
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3 3 0.022 2.35197 0.022 2.35197
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3 5 0.022 2.35197 0.022 2.35197 :pre
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:ule
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This section must have N*(N+1)/2 lines where N = # of atom types. The
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number and meaning of the coefficients are specific to the defined
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pair style. See the "pair_style"_pair_style.html and
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"pair_coeff"_pair_coeff.html commands for details. Since pair
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coefficients for types I != J are all specified, these values will
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turn off the default mixing rule defined by the pair style. See the
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individual pair_style doc pages and the "pair_modify
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mix"_pair_modify.html command for details. Pair coefficients can also
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be set via the "pair_coeff"_pair_coeff.html command in the input
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script.
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:line
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@ -13,9 +13,19 @@
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</H3>
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<P><B>Syntax:</B>
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</P>
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<PRE>write_data file
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<PRE>write_data file keyword value ...
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</PRE>
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<UL><LI>file = name of data file to write out
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<LI>zero or more keyword/value pairs may be appended
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<LI>keyword = <I>pair</I>
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<PRE> <I>pair</I> value = <I>ii</I> or <I>ij</I>
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<I>ii</I> = write one line of pair coefficient info per atom type
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<I>ij</I> = write one line of pair coefficient info per IJ atom type pair
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</PRE>
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</UL>
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<P><B>Examples:</B>
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</P>
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@ -34,15 +44,14 @@ wild-card character. The "*" is replaced with the current timestep
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value.
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</P>
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<P>IMPORTANT NOTE: The write-data command is not yet fully implemented in
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two respects. First, most pair, bond, angle, dihedral, improper
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styles do not yet write their coefficient information into the data
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file. This means you will need to specify that information in your
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input script that reads the data file, e.g. with the
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<A HREF = "pair_coeff.html">pair_coeff</A> command. Second, a few of the <A HREF = "atom_style.html">atom
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styles</A> (body, ellipsoid, line, tri) that store
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auxiliary "bonus" information about aspherical particles, do not yet
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write the bonus info into the data file. Both these functionalities
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will be added to the write_data command later.
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two respects. First, most pair styles do not yet write their
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coefficient information into the data file. This means you will need
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to specify that information in your input script that reads the data
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file, via the <A HREF = "pair_coeff.html">pair_coeff</A> command. Second, a few of
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the <A HREF = "atom_style.html">atom styles</A> (body, ellipsoid, line, tri) that
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store auxiliary "bonus" information about aspherical particles, do not
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yet write the bonus info into the data file. Both these
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functionalities will be added to the write_data command later.
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</P>
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<P>Because a data file is in text format, if you use a data file written
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out by this command to restart a simulation, the initial state of the
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@ -76,6 +85,31 @@ read.
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written to the data file. Thus these bonds will not exist when the
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data file is read.
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</P>
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<HR>
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<P>The <I>pair</I> keyword lets you specify in what format the pair
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coefficient information is written into the data file. If the value
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is specified as <I>ii</I>, then one line per atom type is written, to
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specify the coefficients for each of the I=J interactions. This means
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that no cross-interactions for I != J will be specified in the data
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file and the pair style will apply its mixing rule, as documented on
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individual <A HREF = "pair_style.html">pair_style</A> doc pages. Of course this
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behavior can be overridden in the input script after reading the data
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file, by specifying additional <A HREF = "pair_coeff.html">pair_coeff</A> commands
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for any desired I,J pairs.
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</P>
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<P>If the value is specified as <I>ij</I>, then one line of coefficients is
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written for all I,J pairs where I <= J. These coefficients will
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include any specific settings made in the input script up to that
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point. The presence of these I != J coefficients in the data file
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will effectively turn off the default mixing rule for the pair style.
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Again, the coefficient values in the data file can can be overridden
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in the input script after reading the data file, by specifying
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additional <A HREF = "pair_coeff.html">pair_coeff</A> commands for any desired I,J
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pairs.
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</P>
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<HR>
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<P><B>Restrictions:</B>
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</P>
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<P>This command requires inter-processor communication to migrate atoms
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@ -87,6 +121,8 @@ setup, atom masses initialized, etc).
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</P>
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<P><A HREF = "read_data.html">read_data</A>, <A HREF = "write_restart.html">write_restart</A>
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</P>
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<P><B>Default:</B> none
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<P><B>Default:</B>
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</P>
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<P>The option defaults are pair = ii.
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</P>
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</HTML>
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@ -10,9 +10,15 @@ write_data command :h3
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[Syntax:]
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write_data file :pre
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write_data file keyword value ... :pre
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file = name of data file to write out :ul
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file = name of data file to write out :ulb,l
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zero or more keyword/value pairs may be appended :l
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keyword = {pair} :l
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{pair} value = {ii} or {ij}
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{ii} = write one line of pair coefficient info per atom type
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{ij} = write one line of pair coefficient info per IJ atom type pair :pre
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:ule
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[Examples:]
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@ -31,15 +37,14 @@ wild-card character. The "*" is replaced with the current timestep
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value.
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IMPORTANT NOTE: The write-data command is not yet fully implemented in
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two respects. First, most pair, bond, angle, dihedral, improper
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styles do not yet write their coefficient information into the data
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file. This means you will need to specify that information in your
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input script that reads the data file, e.g. with the
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"pair_coeff"_pair_coeff.html command. Second, a few of the "atom
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styles"_atom_style.html (body, ellipsoid, line, tri) that store
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auxiliary "bonus" information about aspherical particles, do not yet
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write the bonus info into the data file. Both these functionalities
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will be added to the write_data command later.
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two respects. First, most pair styles do not yet write their
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coefficient information into the data file. This means you will need
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to specify that information in your input script that reads the data
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file, via the "pair_coeff"_pair_coeff.html command. Second, a few of
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the "atom styles"_atom_style.html (body, ellipsoid, line, tri) that
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store auxiliary "bonus" information about aspherical particles, do not
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yet write the bonus info into the data file. Both these
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functionalities will be added to the write_data command later.
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Because a data file is in text format, if you use a data file written
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out by this command to restart a simulation, the initial state of the
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@ -73,6 +78,31 @@ Bonds that are broken (e.g. by a bond-breaking potential) are not
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written to the data file. Thus these bonds will not exist when the
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data file is read.
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:line
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The {pair} keyword lets you specify in what format the pair
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coefficient information is written into the data file. If the value
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is specified as {ii}, then one line per atom type is written, to
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specify the coefficients for each of the I=J interactions. This means
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that no cross-interactions for I != J will be specified in the data
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file and the pair style will apply its mixing rule, as documented on
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individual "pair_style"_pair_style.html doc pages. Of course this
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behavior can be overridden in the input script after reading the data
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file, by specifying additional "pair_coeff"_pair_coeff.html commands
|
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for any desired I,J pairs.
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If the value is specified as {ij}, then one line of coefficients is
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written for all I,J pairs where I <= J. These coefficients will
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include any specific settings made in the input script up to that
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point. The presence of these I != J coefficients in the data file
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will effectively turn off the default mixing rule for the pair style.
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Again, the coefficient values in the data file can can be overridden
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in the input script after reading the data file, by specifying
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additional "pair_coeff"_pair_coeff.html commands for any desired I,J
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pairs.
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:line
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[Restrictions:]
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This command requires inter-processor communication to migrate atoms
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@ -84,4 +114,7 @@ setup, atom masses initialized, etc).
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"read_data"_read_data.html, "write_restart"_write_restart.html
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[Default:] none
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[Default:]
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The option defaults are pair = ii.
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